Tutorial: a guide to performing polygenic risk score analyses

Variable prediction accuracy of polygenic scores within an ancestry group

(2020) Hakhamanesh Mostafavi et al.   eLife

Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing

(2019) Brian W. Kunkle et al.   NATURE GENETICS

Polygenic Risk Scores That Predict Common Diseases Using Millions of Single Nucleotide Polymorphisms: Is More, Better?

(2019) A. Cecile J.W. Janssens et al.   CLINICAL CHEMISTRY

Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood

(2019) Amit V. Khera et al.   CELL

On the utilization of polygenic risk scores for therapeutic targeting

(2019) Greg Gibson   PLoS Genetics

A flexible and parallelizable approach to genome‐wide polygenic risk scores

(2019) Paul J. Newcombe et al.   GENETIC EPIDEMIOLOGY

Genetic correlations of polygenic disease traits: from theory to practice

(2019) Wouter van Rheenen et al.   NATURE REVIEWS GENETICS

Analysis of polygenic risk score usage and performance in diverse human populations

(2019) L. Duncan et al.   Nature Communications

Genomic structural equation modelling provides insights into the multivariate genetic architecture of complex traits

(2019) Andrew D. Grotzinger et al.   Nature Human Behaviour

Comparing Within- and Between-Family Polygenic Score Prediction

(2019) Saskia Selzam et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GWAS of Suicide Attempt in Psychiatric Disorders and Association With Major Depression Polygenic Risk Scores

(2019) Niamh Mullins et al.   AMERICAN JOURNAL OF PSYCHIATRY

Towards clinical utility of polygenic risk scores

(2019) Samuel A Lambert et al.   HUMAN MOLECULAR GENETICS

Validity of polygenic risk scores: are we measuring what we think we are?

(2019) A Cecile J W Janssens   HUMAN MOLECULAR GENETICS

Polygenic scores: Are they a public health hazard?

(2019) Keith Baverstock   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Deconstructing the sources of genotype-phenotype associations in humans

(2019) Alexander I. Young et al.   SCIENCE

Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr

(2018) Florian Privé et al.   BIOINFORMATICS

Genomic Dissection of Bipolar Disorder and Schizophrenia, Including 28 Subphenotypes

(2018) Douglas M. Ruderfer et al.   CELL

A tutorial on conducting genome-wide association studies: Quality control and statistical analysis

(2018) Andries T. Marees et al.   INTERNATIONAL JOURNAL OF METHODS IN PSYCHIATRIC RESEARCH

Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits

(2018) Luke M. Evans et al.   NATURE GENETICS

Mixed-model association for biobank-scale datasets

(2018) Po-Ru Loh et al.   NATURE GENETICS

Multi-trait analysis of genome-wide association summary statistics using MTAG

(2018) Patrick Turley et al.   NATURE GENETICS

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals

(2018) James J. Lee et al.   NATURE GENETICS

The personal and clinical utility of polygenic risk scores

(2018) Ali Torkamani et al.   NATURE REVIEWS GENETICS

Using genetic data to strengthen causal inference in observational research

(2018) Jean-Baptiste Pingault et al.   NATURE REVIEWS GENETICS

The nature of nurture: Effects of parental genotypes

(2018) Augustine Kong et al.   SCIENCE

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders

(2018) Mari E. K. Niemi et al.   NATURE

Genome-wide polygenic scores for common diseases identify individuals with risk equivalent to monogenic mutations

(2018) Amit V. Khera et al.   NATURE GENETICS

Polygenic risk score analyses of symptoms and treatment response in an antipsychotic-naive first episode of psychosis cohort

(2018) Marcos Leite Santoro et al.   Translational Psychiatry

Polygenic Risk Scores for Prediction of Breast Cancer and Breast Cancer Subtypes

(2018) Nasim Mavaddat et al.   AMERICAN JOURNAL OF HUMAN GENETICS

SumHer better estimates the SNP heritability of complex traits from summary statistics

(2018) Doug Speed et al.   NATURE GENETICS

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Multiethnic polygenic risk scores improve risk prediction in diverse populations

(2017) Carla Márquez-Luna et al.   GENETIC EPIDEMIOLOGY

Polygenic scores via penalized regression on summary statistics

(2017) Timothy Shin Heng Mak et al.   GENETIC EPIDEMIOLOGY

Predictive accuracy of combined genetic and environmental risk scores

(2017) Frank Dudbridge et al.   GENETIC EPIDEMIOLOGY

Multi-polygenic score approach to trait prediction

(2017) E Krapohl et al.   MOLECULAR PSYCHIATRY

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

(2017) Suzanne Sniekers et al.   NATURE GENETICS

Key steps and common pitfalls in developing and validating risk models

(2016) L Wynants et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

Polygenic Epidemiology

(2016) Frank Dudbridge   GENETIC EPIDEMIOLOGY

Two-sample Mendelian randomization: avoiding the downsides of a powerful, widely applicable but potentially fallible technique

(2016) Fernando Pires Hartwig et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Predicting educational achievement from DNA

(2016) S Selzam et al.   MOLECULAR PSYCHIATRY

Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data

(2016) Jianxin Shi et al.   PLoS Genetics

Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

(2015) Bjarni J. Vilhjálmsson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Fast Method that Uses Polygenic Scores to Estimate the Variance Explained by Genome-wide Marker Panels and the Proportion of Variants Affecting a Trait

(2015) Luigi Palla et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Quality control, imputation and analysis of genome-wide genotyping data from the Illumina HumanCoreExome microarray

(2015) Jonathan R. I. Coleman et al.   Briefings in Functional Genomics

Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression

(2015) J. Bowden et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Phenome-wide analysis of genome-wide polygenic scores

(2015) E Krapohl et al.   MOLECULAR PSYCHIATRY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Genetic studies of body mass index yield new insights for obesity biology

(2015) Adam E. Locke et al.   NATURE

An atlas of genetic correlations across human diseases and traits

(2015) Brendan Bulik-Sullivan et al.   NATURE GENETICS

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

(2015) Brendan K Bulik-Sullivan et al.   NATURE GENETICS

Polygenic risk scores for schizophrenia and bipolar disorder predict creativity

(2015) Robert A Power et al.   NATURE NEUROSCIENCE

Polygenic interactions with environmental adversity in the aetiology of major depressive disorder

(2015) N. Mullins et al.   PSYCHOLOGICAL MEDICINE

Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease

(2015) Hong-Hee Won et al.   PLoS Genetics

UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age

(2015) Cathie Sudlow et al.   PLOS MEDICINE

Polygenic Risk Score, Parental Socioeconomic Status, Family History of Psychiatric Disorders, and the Risk for Schizophrenia

(2015) Esben Agerbo et al.   JAMA Psychiatry

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

PRSice: Polygenic Risk Score software

(2014) Jack Euesden et al.   BIOINFORMATICS

How to Include Chromosome X in Your Genome-Wide Association Study

(2014) Inke R. König et al.   GENETIC EPIDEMIOLOGY

MultiBLUP: improved SNP-based prediction for complex traits

(2014) Doug Speed et al.   GENOME RESEARCH

Research Review: Polygenic methods and their application to psychiatric traits

(2014) Naomi R. Wray et al.   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

Statistical Power to Detect Genetic (Co)Variance of Complex Traits Using SNP Data in Unrelated Samples

(2014) Peter M. Visscher et al.   PLoS Genetics

Polygenic dissection of diagnosis and clinical dimensions of bipolar disorder and schizophrenia

(2013) D M Ruderfer et al.   MOLECULAR PSYCHIATRY

Pitfalls of predicting complex traits from SNPs

(2013) Naomi R. Wray et al.   NATURE REVIEWS GENETICS

Power and Predictive Accuracy of Polygenic Risk Scores

(2013) Frank Dudbridge   PLoS Genetics

Polygenic Modeling with Bayesian Sparse Linear Mixed Models

(2013) Xiang Zhou et al.   PLoS Genetics

A Better Coefficient of Determination for Genetic Profile Analysis

(2012) Sang Hong Lee et al.   GENETIC EPIDEMIOLOGY

Link Functions in Multi-Locus Genetic Models: Implications for Testing, Prediction, and Interpretation

(2012) David Clayton   GENETIC EPIDEMIOLOGY

Including known covariates can reduce power to detect genetic effects in case-control studies

(2012) Matti Pirinen et al.   NATURE GENETICS

Estimating Missing Heritability for Disease from Genome-wide Association Studies

(2011) Sang Hong Lee et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Random-Effects Model Aimed at Discovering Associations in Meta-Analysis of Genome-wide Association Studies

(2011) Buhm Han et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Data quality control in genetic case-control association studies

(2010) Carl A Anderson et al.   Nature Protocols

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Population Structure and Cryptic Relatedness in Genetic Association Studies

(2010) William Astle et al.   STATISTICAL SCIENCE

Outlier and influence diagnostics for meta-analysis

(2010) Wolfgang Viechtbauer et al.   Research Synthesis Methods

Common polygenic variation contributes to risk of schizophrenia and bipolar disorder

(2009) Shaun M. Purcell et al.   NATURE

Prediction and Interaction in Complex Disease Genetics: Experience in Type 1 Diabetes

(2009) David G. Clayton   PLoS Genetics